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- EMDB-3660: 601 nucleosome -

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Basic information

Entry
Database: EMDB / ID: EMD-3660
Title601 nucleosome
Map data601 nucleosome
Sample
  • Complex: 601 nucleosome
Biological speciesXenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 11.4 Å
AuthorsBednar J / Garcia-Saez I / Boopathi R / Cutter AR / Papai G / Reymer A / Syed SH / Lone IN / Tonchev O / Crucfix C ...Bednar J / Garcia-Saez I / Boopathi R / Cutter AR / Papai G / Reymer A / Syed SH / Lone IN / Tonchev O / Crucfix C / Menoni H / Papin C / Skoufias DA / Kurumizaka H / Lavery R / Hamiche A / Hayes JJ / Schultz P / Angelov D / Petosa C / Dimitrov S
CitationJournal: Mol Cell / Year: 2017
Title: Structure and Dynamics of a 197 bp Nucleosome in Complex with Linker Histone H1.
Authors: Jan Bednar / Isabel Garcia-Saez / Ramachandran Boopathi / Amber R Cutter / Gabor Papai / Anna Reymer / Sajad H Syed / Imtiaz Nisar Lone / Ognyan Tonchev / Corinne Crucifix / Hervé Menoni / ...Authors: Jan Bednar / Isabel Garcia-Saez / Ramachandran Boopathi / Amber R Cutter / Gabor Papai / Anna Reymer / Sajad H Syed / Imtiaz Nisar Lone / Ognyan Tonchev / Corinne Crucifix / Hervé Menoni / Christophe Papin / Dimitrios A Skoufias / Hitoshi Kurumizaka / Richard Lavery / Ali Hamiche / Jeffrey J Hayes / Patrick Schultz / Dimitar Angelov / Carlo Petosa / Stefan Dimitrov /
Abstract: Linker histones associate with nucleosomes to promote the formation of higher-order chromatin structure, but the underlying molecular details are unclear. We investigated the structure of a 197 bp ...Linker histones associate with nucleosomes to promote the formation of higher-order chromatin structure, but the underlying molecular details are unclear. We investigated the structure of a 197 bp nucleosome bearing symmetric 25 bp linker DNA arms in complex with vertebrate linker histone H1. We determined electron cryo-microscopy (cryo-EM) and crystal structures of unbound and H1-bound nucleosomes and validated these structures by site-directed protein cross-linking and hydroxyl radical footprinting experiments. Histone H1 shifts the conformational landscape of the nucleosome by drawing the two linkers together and reducing their flexibility. The H1 C-terminal domain (CTD) localizes primarily to a single linker, while the H1 globular domain contacts the nucleosome dyad and both linkers, associating more closely with the CTD-distal linker. These findings reveal that H1 imparts a strong degree of asymmetry to the nucleosome, which is likely to influence the assembly and architecture of higher-order structures.
History
DepositionApr 4, 2017-
Header (metadata) releaseMay 17, 2017-
Map releaseMay 17, 2017-
UpdateJul 12, 2017-
Current statusJul 12, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.006
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.006
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3660.png

Downloads & links

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Map

FileDownload / File: emd_3660.map.gz / Format: CCP4 / Size: 28.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation601 nucleosome
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.78 Å/pix.
x 196 pix.
= 348.88 Å		1.78 Å/pix.
x 196 pix.
= 348.88 Å		1.78 Å/pix.
x 196 pix.
= 348.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.78 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.006 / Movie #1: 0.006
Minimum - Maximum-0.029442614 - 0.071102045
Average (Standard dev.)0.000000000000695 (±0.0025464832)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-102-102-102
Dimensions196196196
Spacing196196196
CellA=B=C: 348.88 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.781.781.78
M x/y/z196196196
origin x/y/z0.0000.0000.000
length x/y/z348.880348.880348.880
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-102-102-102
NC/NR/NS196196196
D min/max/mean-0.0290.0710.000

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Supplemental data

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Sample components

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Entire : 601 nucleosome

EntireName: 601 nucleosome
Components
  • Complex: 601 nucleosome

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Supramolecule #1: 601 nucleosome

SupramoleculeName: 601 nucleosome / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.3 mg/mL
BufferpH: 7.2
GridModel: Quantifoil R2/2 / Material: COPPER/RHODIUM / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: FEI FALCON I (4k x 4k) / Average exposure time: 1.0 sec. / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 100 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 78652 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal magnification: 59000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 94264
CTF correctionSoftware - Name: CTFFIND (ver. 3)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 11.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 29222
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.3)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4)
Final 3D classificationNumber classes: 5 / Software - Name: RELION (ver. 1.4)

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